While the gap in test scores is small, University of Melbourne researchers say it's equivalent to a grade 3 student missing up to 35 days of school.

And they suspect different bacteria in the guts of babies delivered by caesarean could be behind the delay.

In a world-first study, researchers measured the cognitive performance of 5000 Australian children who were born vaginally and via caesarean using NAPLAN results and data from the Longitudinal Study of Australian Children.

The findings show correlation not causation, but were surprising to the study's co-author, Dr Cain Polidano???.

Children born via c-section had small delays in their grammar, numeracy, reading and writing skills between the ages of four to nine, he said.

"We see this consistently in the data," he said. "It is not clear whether those differences will close or open up."

The study, which was published in the peer-reviewed journal Scientific Reports on Wednesday evening, is likely to surprise thousands of parents with clever children born via caesarean.

It's a sensitive issue. Only a tiny proportion of women want to have a caesarean.

But the number of babies delivered via caesarean has increased worldwide - fuelled by a rise in obesity, women having children at a later age and a more risk-averse society.

Australia has a 33 per cent caesarean rate compared to the World Health Organisation recommendation of a maximum of 15 per cent.

The researchers said they did not want to put extra pressure on parents already facing difficult decisions.

Dr Polidano hopes it triggers discussion about the risks of caesarean births.

"A lot of women have misconceptions about what a caesarean is - it is major surgery," he said "We believe our findings point to the need for a more precautionary approach to requests for planned caesarean births."

But he said providing children with a healthy, supportive home life always trumped any differences that arose from caesarean delivery.

Dr Polidano has two sons, aged 12 and 14, who were born via caesarean and he said they were doing well at school.

Professor Joel Bornstein???, a neurophysiologist who co-authored the research, suspects that differences in babies' gut bacteria could be behind the delay.

The guts of babies born vaginally are colonised by bacteria ingested from their mother's vagina and fecal matter, while the guts of those born via c-section are colonised by bacteria from their mother's skin and hospital surfaces.

"The bacteria species that colonise the gut are quite different between the two populations," Professor Bornstein said.

Research involving mice shows that differences in gut bacteria impact their cognitive development, he said.

"The gut and the brain speak to each other," he said.

The research is not conclusive enough to trigger changes to birthing practices, according to Dr Charlotte Elder from the Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

"All we can draw from it is that it is something that needs to be looked at further," she said.

"With something this complicated, before having a major practice change, you would want multiple studies suggesting the same thing."

The researchers tested the robustness of their results by excluding mothers with elevated health risks which led to caesareans and could impact a child's development. But the results remained the same.

Dr Elder, who is the honorary secretary of the college's Victorian and Tasmanian regional committee, said many women who requested elective caesareans had experienced previous trauma including sexual abuse, or suffered anxiety issues.

Australian College of Midwives council chair Rebekah Bowman said there was still a lot of guilt around having a caesarean. She said it was important that women were provided with as much information as possible.

"A well-informed woman is one who knows the potential outcomes of however she gives birth," she said.

Ms Bowman said midwives spoke to women about the importance of babies travelling down the vaginal canal and ingesting bacteria.

"We know it's beneficial for their immune system and they would miss out on that with a caesarean birth," she said.